Genomic insights into the ancestry and mortality of a historical era population from Southwest China

Abstract

The Yun-Gui (Yunnan and Guizhou) Plateau of Southwest China has long been characterized by long-standing ethnolinguistic diversity shaped by complex demographic history. Although numerous groups belonging to distinct language families have inhabited the region over recent centuries, the nature and extent of their interactions remain poorly understood. At a natural karst cave located in a multiethnic area of southern Guizhou, archaeologists uncovered scattered skeletal remains of several dozen individuals dated to the late Yuan and early Ming dynasties (575–685 cal BP). The genetic origins of these individuals and the context of their deaths were previously unknown. Here, we present genome-wide ancient DNA analysis from 22 individuals recovered from the cave. The results reveal a strikingly genetically homogeneous population, exhibiting admixed ancient northern and southern East Asian ancestry, yet showing clear genetic differentiation from contemporaneous neighboring groups. This ancestry profile represents a genetic component that contributed to present-day ethnolinguistic groups in Southwest China. Genetic kinship analyses indicate that the group comprised several family units and was dominated by females. Furthermore, we detected authentic Salmonella enterica (S. enterica) DNA in one individual, supported by high sequence similarity to reference genomes of serovars S. Choleraesuis and S. Paratyphi C, along with characteristic ancient DNA damage patterns. No similar pathogen DNA was identified in other individuals. Integrating genomic evidence with historical records, we infer that these individuals most likely represent collective mortality associated with conflict rather than a widespread epidemic.